Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_21

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cd08520: PBP2_NikA_DppA_OppA_like_21 
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.
This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 173885
View PSSM: cd08520
Aligned: 16 rows
Threshold Bit Score: 573.882
Threshold Setting Gi: 119384348
Created: 7-Feb-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
YP_842941     27 VYTIADttgdwgyPSPYLhysrGPGYVrmsfiFDTLVWKDq-nGFVPALAESWEYlkdenAYIFNLNPnAKWHDGEPFTA 105 Methanosaeta th...
YP_001212038  44 SYTIADptgdwgfPSPYAhyarGPGYVrmsfiFDTLIWKDd-kGYVPALAESWEYlkeenAYLFKLRRdATWHDGQKFKA 122 Pelotomaculum t...
YP_915404     27 PLIITDsradrgmLAPYLhtrnGIAYLymtyvFDSLVSQDrqgRPAPGLAASWTIsadglTADLQMDGrASWHDGRPVTA 106 Paracoccus deni...
ZP_01665807   38 PVTLKIaaedygyPSPYTfyprGPGYIrmsllFDTLVWKDq-kGVIPWLSERYEVskdgrEWVFYLHPgVKWHDGQPLTA 116 Thermosinus car...
YP_001680442  23 TYTIADprgdwgfPSPWGhyqrGPGYLrmsflYDTLIWKDe-qGFTPALASHWSYdegtkAYRFALRDdALWHDGQKVTA 101 Heliobacterium ...
NP_907347     27 EIRIGDsqgdfgyPNPYQhyprGPGYVrmswvFDTLIWKDr-sGFRGALAKEWRYdeknrTFIFLLQPeAKWHDGHSVSA 105 Wolinella succi...
AAU83930      28 TYIIADptgdwgyPTPHGhyprGPGYVrmsliFDTLVWKDt-qSFVPALATDWEYledenAYLFHLRKgVTWHDGEEFTA 106 uncultured arch...
YP_001781302  48 NIKLEGgdw--gePNPYKtyprGPGMSktnliYDSLIEKDe-kRIIPWLAEKWEVksngkEYLFKIREgVKWQDGKAFTP 124 Clostridium bot...
NP_615799     64 VAYLSGgdy--gyPQPFTiyprGPGSSkvgmiFDSLLERDe-vGIIPWLGESWDVsedgtEYTFHLRQgVTWSDGEPFTA 140 Methanosarcina ...
YP_001435607  15 ASALSVglgdwglPTPFSfyprGPGYVltsfsFDTLVWKDe-rGVIPWLAYKWEAng--tAVKFYLRE-AKWSDGEPLTA 90  Ignicoccus hosp...
YP_842941    106 DDVVFTINYIKEHpyqwvd-----sstvdrAEKIDDHTVKIYlakpyaPFLDQvagtlpILPEHIYIDVTKPEDFQDAka 180 Methanosaeta th...
YP_001212038 123 ADVAFTFDYMKKHpyqwvd-----tsivkrAEAIDEYTVKLYldktyaPFLDFiagtvpILPEHVWKEVENPEQFQQKea 197 Pelotomaculum t...
YP_915404    107 RDAAFTFAYMARHpypfvt-----lknvagAEALSDRHLRITlksrdaGLVSGlltalpILPEHVYAAEDAPERFTAPea 181 Paracoccus deni...
ZP_01665807  117 EDVKFTFEYIRSHphpwysr---einiiesIEAINAQQVRLTlktpyaPFLTNiaatipIIPKHIWQTVSDPMKFTDPta 193 Thermosinus car...
YP_001680442 102 GDVLFTFEYMKKHpypwvd-----lsevekVEAVDAQTVQITlkrhyaPFLENvagalpILPRHIWAAIERPEEHAEKev 176 Heliobacterium ...
NP_907347    106 EDVAFTVDYFRRHpyfwvd-----vsaierVEVKSPHEVHFHllrpysPFLSDiggtmpILPKHIWAGVENPKTFLSKea 180 Wolinella succi...
AAU83930     107 EDVAFTYNYVKEHpswwvd-----lkslkqAEVLDEYTVKIYlneryaPFLNNdagtlaILPKHIWQDVVDPAEFREPes 181 uncultured arch...
YP_001781302 125 EDVKFTFDYYKKHppvskniyigkkcfidkVEVLKDNYIKITvntvnaASLENlgt-trIIPKHIWEKVEDPKKFDGKea 203 Clostridium bot...
NP_615799    141 NDVKFTFDYEQENvpisggi---esgvidnVQVVDSNTVKFVlkqpvsTFLYKlts-fkIIPEHIYENVSDPFSFLDPea 216 Methanosarcina ...
YP_001435607  91 EDVVFTFKYLMKHgwhwkni---pkdlikdVKALDDRTVVVElsrpfpFFVEEyattvfVLPKHVWEKVKDPFSYRGKda 167 Ignicoccus hosp...
YP_842941    181 LTGTGPFKLVDYNKaqGTYLYEANEDYYqgAPKVKQLKFVKlsee---magpALKRGEVDAAAvppevae------glrg 251 Methanosaeta th...
YP_001212038 198 LIGTGPFKLVDYNKeqGTYLYERYEQYYqgQPKVRQLKFIKigaemataalrQKQADMAQVPPeiakel--------eke 269 Pelotomaculum t...
YP_915404    182 ATGSGPYRLASYDKaqGRYMLEAVPDHYagAPKFTRLMIVTmapd---aairALRGGEVDVISdlpveraa---gveaqg 255 Paracoccus deni...
ZP_01665807  194 VIGSGPFKLVKYDKaaSLYIYEANPQYFkgRVKIGRLVFTWpgq-----pllAFQNGEVDAFNpdadqvav----lkggk 264 Thermosinus car...
YP_001680442 177 LIGSGPYRLVDYSKehGTYLYQANDRYYggKPKVAQIRFVKlnes---maaaALTKGEVDAAQipgetae-----qmrqv 248 Heliobacterium ...
NP_907347    181 FIGSGPYRYVDFDKvkGSYLYEAFEGYYggKPKAKRLLYVRsdk-----plnALLAGQIHLAGikptmqem----iqknp 251 Wolinella succi...
AAU83930     182 LIGTGPFKLVDYSKthGTYLYEVNKDYYrgKPDIDSLKFVKisee---msatALMKNEVPATAilpetva-----evgaa 253 uncultured arch...
YP_001781302 204 FIGCGPYMLEDYNKerGSYKFTAFEDYWgpKQNVKTIEFIPvsd-----silAFEKGDIDLVEsvkpdiak---kyennk 275 Clostridium bot...
NP_615799    217 VTGTGPFLLGEYNKehGTYRFITNEDFWgpETAVKTVEFIPvsd-----sliAFEQGQIDFTSispdtldr----ftsds 287 Methanosarcina ...
YP_001435607 168 FVCSGPYVLKEYVPg-SRYVFVRNPFFWgpKPKYEELVVSAvgpfqpqkavaALIRGEVDSVSlfgkayrlvelakrakp 246 Ignicoccus hosp...
YP_842941    252 sfVVLEGAHdWLAKLMINhkke-pfsDVRFRQALAYSIDREKLVEIAQr-GYGVPas-pGLFAPdsewy-npdvEQYAHD 327 Methanosaeta th...
YP_001212038 270 gfKVLAIAHdWVAKLMINhqkd-plnNRELRQALAFAIDRQALVDTAQr-GYALAgs-pGLVPPdsdwyntrldGKYPAD 346 Pelotomaculum t...
YP_915404    256 lhVVRARSG-HVTKIAFNhqg--mfgARTLRQALAQALDRLAILDITApnGAGALae-tGYFQQgspwredrtdPVWPHD 331 Paracoccus deni...
ZP_01665807  265 nvKIIEGSGfWIFRLMFNlaqh-pfdQLEFRQAVAYALNLPEIVSRATh-GGATPgn-pGYLSPelgewynprvATYPYD 341 Thermosinus car...
YP_001680442 249 gmQVIRGPHfWNAKLMFNhqka-pfsDKAFRQALAYTIDRQELVAKSLr-GQGAPas-pGLIPPdspwh-epqvTPYTAD 324 Heliobacterium ...
NP_907347    252 nlKIIEDEKgWTKKLMINhrrp-llnERSFRQALSYAIDREELIAKSQq-GEAYLas-lGLLSSdhaff-apnlPAYAYN 327 Wolinella succi...
AAU83930     254 gfVIINQSGnWNAKLMINhnka-pmsSKEFRHALAYAINRTELVEIAQr-GHAIQgs-pGLLSPttpyy-npniPYYEYD 329 uncultured arch...
YP_001781302 276 eyKLIKGHNfFGYRLCLNmnknpefkDKNVRQAIAYAIDEKEIIDKVMr-GIGTEgs-aAYLPKehiwy-nkdiKKYDYN 352 Clostridium bot...
NP_615799    288 diRVVQQPAfWGYQFYFNmkecpelnDSKIRQAFAYAIDRGELVEKIAr-GAGKPge-mGILPEdhiwy-npdqPEYSYD 364 Methanosarcina ...
YP_001435607 247 dlIVKRGPSyWVLFLGFNldee-pysFKEFRKAVAMSLDLKELVELSAg-PGAAEpgspGYVPPysrfy-eddvPKYRYD 323 Ignicoccus hosp...
YP_842941    328 PEKAGELLKELGYekkgvff---ekdgktlEVELLVTss--------nERAGELIKRDLEEAGIKVNMRs-vDSKTLDNA 395 Methanosaeta th...
YP_001212038 347 PARAAEILASLGYvkngsyf---ekdgrplELELLFSgggggvlgspgEREAEMIKAQLERAGIKVNLRs-lESKTLDSR 422 Pelotomaculum t...
YP_915404    332 PAIAATLFEAQGFarngtgrw--qrdgapvTLRLISDes--------qARVAQVVADQLEGFGFGVELRl--MERTALQA 399 Paracoccus deni...
ZP_01665807  342 PEKARNLLTGLGYtqigpdgirrapdgkrlSFELLTFq---------qGQDGEIVKNMLAAVGIDVRIKa-mEKGAHDQL 411 Thermosinus car...
YP_001680442 325 LEKARELLASLGYfleqgsl---vkecrelSLELLCSpd--------nGRDGEIIKEQLARIGIKVRVKs-lEAKTVDAK 392 Heliobacterium ...
NP_907347    328 PQKAKEILASLGYqpnregkm--ekegkplKLQLLTStitag-gqagsDRDGEMIQKMLERIGITVELLa-lESTTLDLR 403 Wolinella succi...
AAU83930     330 PERAKDILEGQGYqlkedgyy--wkdgevlELELITAsrf------gfERVAEIIARQLEDIGIKVNLRs-lEWKTLDSR 400 uncultured arch...
YP_001781302 353 VEKAKELLKGKNI-----------------TFQIIVSnkk------dnLRMAELLKLQLEKTGMKVNVKs-iDMKSRDAA 408 Clostridium bot...
NP_615799    365 PDTAGALLEEAGWtdtdgdgi-rdkngeqlSYVLSLSsg--------eVRIGELIKERLSEVGVDVQVKa-lESKSRDTN 434 Methanosarcina ...
YP_001435607 324 PEAAARLLKSVGVedvngdgcaefrgrpwrPLLVTTKq---------fVQEALIVKKMLKRVKICVNVKvvpGPKQLDLI 394 Ignicoccus hosp...
YP_842941    396 VNEw-nFDLALSGHggmggDPAILNKVItgsgfn--------sarydNQELSDLLKREisemDPEKRRELVNEIQEVYAR 466 Methanosaeta th...
YP_001212038 423 VNDw-kFDLALSGHgglggDPEFLNKVIagkgfl-------saryqeNEELNQMLKQQlslmDKERRKELVAKIQEIYAE 494 Pelotomaculum t...
YP_915404    400 VPPggdYDLLIASVsttgdPGDIASRVTgdawsa--------dryagDGRIAAALEAArqaaTPEKRLAHLRAFQRLYAE 471 Paracoccus deni...
ZP_01665807  412 IDSg-qYQMALNGHggiggDPVFLNQLIkpltavk-----dnptlynNPEYIRLARQQtamiDKNERRQAVFKMQEILAN 485 Thermosinus car...
YP_001680442 393 VGAw-dFDLAVSGHggiggDPQFFSRMItgqgfl-------saryndNSRLNALLNEQlsamDEEKRKEQVREAQRIYAE 464 Heliobacterium ...
NP_907347    404 VKNw-eFDLAVSGHggisgDAKILNEMIspnegags---vnsarfegNARLNELLRLQieemNPSKRQELVQEIQQLHAL 479 Wolinella succi...
AAU83930     401 VITr-qFDLAVSGHggiggDPAILNKVIlgnfgy-------sanytkNDTLNQLLEAQlhemDEEKRKEMVQEIQKVYAE 472 uncultured arch...
YP_001781302 409 VKSg-dYEAIITEHggwgkDADVLRELYksnndknggsvingipgykNEEIDKLCMKQmqemDPDKRKEIIFQLQEKIAE 487 Clostridium bot...
NP_615799    435 LKNg-dFELLISGFggwgkDADYLRTRYcdttesgsvssgaavfgyhNDTLNALGSQElqelDDDKRKEIVYDMQTVLSN 513 Methanosarcina ...
YP_001435607 395 VKGg-gYGFVISGHgavgnDPLAAAWWFerfs-----------apwrDPRYLELARELlnapSAEEAIKVVKEIQRLVAE 462 Ignicoccus hosp...
YP_842941    467 eLPALPLYYPtnYWAHDG-KVDLF 489 Methanosaeta thermophila PT
YP_001212038 495 eMPCMPLYYPnwYYAHDG-KVNLY 517 Pelotomaculum thermopropionicum SI
YP_915404    472 eLPSLMLIDPvmASAHGG-RIALE 494 Paracoccus denitrificans PD1222
ZP_01665807  486 dLPTIPLYYRkmYFAYRPdKLDGW 509 Thermosinus carboxydivorans Nor1
YP_001680442 465 dLPALSLYYPtdYWCHNG-KVNLF 487 Heliobacterium modesticaldum Ice1
NP_907347    480 eLPAIPLYYPksLTAFDT-RLGVE 502 Wolinella succinogenes DSM 1740
AAU83930     473 eLPALTLYYPtwYWGHDG-SVDIY 495 uncultured archaeon GZfos35A2
YP_001781302 488 eIPMIPIINTssISVHKTdKYDGY 511 Clostridium botulinum B1 str. Okra
NP_615799    514 dVPAIPLYYTtsYDVWRIsKYDGW 537 Methanosarcina acetivorans C2A
YP_001435607 463 eLPRIALYYPyqFLLDSS-RAGWF 485 Ignicoccus hospitalis KIN4/I
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